The Transcriptome of Prematurely Aging Yeast Cells Is Similar to That of Telomerase-deficient Cells

Abstract

To help define the pathologies associated with yeast cells as they age, we analyzed the transcriptome of young and old cells isolated by elutriation, which allows isolation of biochemical quantities of old cells much further advanced in their life span than old cells prepared by the biotin-streptavidin method. Both 18-generation-old wild-type yeast and 8-generation-old cells from a prematurely aging mutant (dna2-1), with a defect in DNA replication, were evaluated. Genes involved in gluconeogenesis, the glyoxylate cycle, lipid metabolism, and glycogen production are induced in old cells, signifying a shift toward energy storage. We observed a much more extensive generalized stress response known as the environmental stress response (ESR), than observed previously in biotin-streptavidin-isolated cells, perhaps because the elutriated cells were further advanced in their life span. In addition, there was induction of DNA repair genes that fall in the so-called DNA damage "signature" set. In the dna2-1 mutant, energy production genes were also induced. The response in the dna2-1 strain is similar to the telomerase delete response, genes whose expression changes during cellular senescence in telomerase-deficient cells. We propose that these results suggest, albeit indirectly, that old cells are responding to genome instability. INTRODUCTIONMuch aging research is aimed at identifying the processes that lead to the generation of age-related cellular damage and understanding exactly how and where this damage occurs. Recently, there has been renewed focus on model organisms, such as the budding yeast Saccharomyces cerevisiae, for experimental work on aging. Yeast provides a model for contributions to aging made by tissues and organs that consist of constantly proliferating cells, replicative aging. Yeast has many advantages for replicative aging studies, such as its short life span, completely sequenced genome, and well-characterized biology. Individual yeast cells are mortal, and their life span is measured by the number of times they divide, i.e., the number of daughter cells produced by a single mother (Mortimer and Johnston, 1959;Muller et al., 1980). These daughter cells have the potential for a full life span, whereas the mother cell increases in age with each cell division; thus, yeast aging is asymmetric. The probability that an individual yeast cell will produce daughters declines exponentially as a function of its age in cell divisions or generations (Jazwinski et al., 1998). As yeast cells age, their size increases (Mortimer and Johnston, 1959;Nestelbacher, 2000), their cell cycle slows down (Mortimer and Johnston, 1959), their shape is altered (Pichova et al., 1997), their nucleolus tends to be larger and/or more fragmented, and they become sterile (Guarente, 1997). In wild-type cells, extrachromosomal ribosomal DNA circles (ERCs) also accumulate . Cells in the second half of their life span also show a switch to a state inducing increase loss of heterozygosity (LOH) (McMurray and Gottschling, 2003). Although...

Single cell metabolomics

“…For example, from population-level metabolomic measurements on cellcycle-synchronized yeast cells, it was found that significant changes in gene regulation and metabolite levels occur during the cell cycle [14]. Also, the age of a yeast cell was argued to influence the metabolic phenotype in clonal cells: In cells that were sorted according to their age, dramatic metabolic differences were found [15][16][17]. Synchronizing as well as sorting cells likely affects the metabolome, due to fast metabolic turnover rates.…”

Changes in Transcription and Metabolism During the Early Stage of Replicative Cellular Senescence in Budding Yeast

“…In addition, the expression of ribosome genes and genes involved in protein synthesis, folding, and degradation all decreased (14,15). Besides changes in metabolic gene expression, environmental stress response genes were induced in aged cells (7), although oxidative stress gene expression did not change (14). Genes involved in DNA damage repair such as homologous recombination and nucleotide excision repair were also induced in old cells (7,15).…”

“…Several transcriptome analyses comparing old cells with young cells have shown pathway changes in expression during replicative aging (7,(13)(14)(15). In all cases, a shift from glycolysis toward gluconeogenesis and energy storage (glyoxylate cycle, lipid metabolism, and glycogen production) was observed in old cells.…”

“…The replicative lifespan of a yeast cell is defined as the number of daughter cells that a mother cell can generate before dying (6). The median replicative lifespan of most wild-type strains is ϳ25 generations; the maximum recorded is ϳ40 generations (7). Yeast cells age as they undergo division, as do cultured mammalian cells: their size increases, their shape is altered, their cell cycle slows down, and they become sterile (8).…”

“…Besides changes in metabolic gene expression, environmental stress response genes were induced in aged cells (7), although oxidative stress gene expression did not change (14). Genes involved in DNA damage repair such as homologous recombination and nucleotide excision repair were also induced in old cells (7,15). These transcriptome studies examined 18 -20-generation-old yeast cells (i.e.…”